2016-07-13

A shiny app for exploring soybean milestone cultivars

  • Explore genetic signatures, genealogy and phenotypic changes of soybean breeding
  • Ultimate task is to understand how the genome changed with the breeding of lines, and how this affected other traits

Data: three sources

  • Next-generation sequencing DNA-seq on 79 lines: DNA sequencing libraries were prepared using TruSeq DNA sample prep and NuGENs unamplified prep kits (Illumina Inc., San Diego, CA and NuGEN Technologies Inc., San Carlos, CA).
  • Field yield trials: 30/79 + 138 ancestral lines
  • Breeding literature, what lines were bred to produce what line

Three apps

  • Copy number variation (CNV): 2Gb of analysis files, annotations
  • SNPs: 12Gb of data, 20mill SNPs, 1mil locations, 79 lines
  • Genealogy: Shows the parent to child lineage

CNV app

  • Seven tabs containing different functionality
  • Four of the tabs, CNV Location, Copy Number, "Search CNVs by Location", and CNV List, primarily concerned with exploring the identified copy number variants
  • The other three tabs, Phenotype Data, Genealogy, and Methodology provide additional information about the soybean cultivars and the experimental methodology
  • App written by Dr Susan Vanderplas

Software

  • shiny: provides the infrastructure, web interface
  • ggplot2: static plots
  • animint: interactive plots

Main page

Your turn

What does copy number variation mean?

Barcode plots

Field trial data

Lineage

Your turn

Your turn

  • Has yield increased over the years?
  • What is the relationship between yield and protein?
  • What is the name of the line that is a recent development, and was sequenced in the study?
  • Find a line who's yield is lower than both parents.

(Hint: Use the Field Trials tab.)

Your turn

  • Is Conrad a descendant of Essex?
  • Who are the grandparents of Essex?
  • How is Illini related to Lawrence?

(Hint: Use the Genealogy tab.)

Your turn

Find some locations on the genome that Lawrence might have inherited from Illini.

(Hint: Use the Barcode plots.)

SNP app

  • Five tabs containing different functionality
  • Overview, SNP locations, search by id, SNP browser, SNP distance and the Kevin Bacon distance
  • App written by Susan Vanderplas

Browse SNPs

Quick overview of three other shiny apps

PeLiCa - peptide library calculator

https://erichare.shinyapps.io/pelica/

  • interactive tool to help plan an experiment
  • What is the baseline probability that a peptide of length p is included in a synthetic library of size N (really large)?
  • What role does peptide encoding play?

Expected Coverage

Creating a logo plot

Matching Bullets

Your turn

Resources

Share and share alike

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